view test-data/BUSTED/gene1.json @ 0:dd2d60b55e0d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drhip commit 15c654c3d27df68a47483031961ace7f5b8d998d

{
 "Evidence Ratios":{
  },
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  ],
 "analysis":{
   "authors":"Sergei L Kosakovsky Pond",
   "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71, *Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril*, Mol Biol Evol. 37(8):2430-2439",
   "contact":"[e-mail]",
   "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted  jointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. Assuming there is evidence of positive selection (i.e. there is an omega > 1),  BUSTED will also perform a quick evidence-ratio style analysis to explore which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, and relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2).\n                               \nVersion 2.1 adds a grid search for the initial starting point.\n\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead. \n\nVersion 3.0 implements the option for branch-site variation in synonymous substitution rates. \n\nVersion 3.1 adds HMM auto-correlation option for SRV, and binds SRV distributions for multiple branch sets.\n\nVersion 4.0 adds support for multiple hits (MH), ancestral state reconstruction saved to JSON, and profiling of branch-site level support for selection / multiple hits.\n\nVersion 4.2 adds calculation of MH-attributable fractions of substitutions.\n\nVersion 4.5 adds an 'error absorption' component \n\nVersion 4.6 adds support for MSS-type models\n",
   "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
   "settings":{
     "error-sink":1,
     "mss":"No",
     "multiple-hit":"None",
     "srv":"Yes"
    },
   "version":"4.6"
  },
 "background":1,
 "branch attributes":{
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    }
  },
 "fits":{
   "MG94xREV with separate rates for branch sets":{
     "AIC-c":1127.910850580984,
     "Equilibrium frequencies":      [
[0.04024763514913952],
      [0.01922996663172304],
      [0.03420070900547616],
      [0.014368896284083],
      [0.03368306905822573],
      [0.01609347460151461],
      [0.02862242313127222],
      [0.01202526618107644],
      [0.03424262136543949],
      [0.01636082378008254],
      [0.02909790661151763],
      [0.01222503317454278],
      [0.04878002735358049],
      [0.02330666869812213],
      [0.04145116886040549],
      [0.01741506429336918],
      [0.01835841860430346],
      [0.008771491191067078],
      [0.0156001944004883],
      [0.006554179193076294],
      [0.01536407988586604],
      [0.007340822446772941],
      [0.01305573416590236],
      [0.0054851637757677],
      [0.0156193121609741],
      [0.007462770186447074],
      [0.01327261957388795],
      [0.005576284808737427],
      [0.02225035479396483],
      [0.01063102412468302],
      [0.01890739435390807],
      [0.007943647847477694],
      [0.02003764925766833],
      [0.009573812850750063],
      [0.01702713237376286],
      [0.007153685002693248],
      [0.01676942064321455],
      [0.008012281919357385],
      [0.01424993228754379],
      [0.005986887554352669],
      [0.01704799882132915],
      [0.008145384126471394],
      [0.01448665603962682],
      [0.006086343359234239],
      [0.02428557790460417],
      [0.01160343585423386],
      [0.0206368394035431],
      [0.008670247303157035],
      [0.01086675715317312],
      [0.008119790817560615],
      [0.01903413243710357],
      [0.009094341326464849],
      [0.01617438694822276],
      [0.006795417266946891],
      [0.009245418998841326],
      [0.01644308026470771],
      [0.006908304587387538],
      [0.02756534742509875],
      [0.0131704809291841],
      [0.02342384645525713],
      [0.009841164995614077]
      ],
     "Log Likelihood":-535.0231635224093,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *background*":        [
[0.2332468645873907, 1]
        ],
       "non-synonymous/synonymous rate ratio for *test*":        [
[0.05436826671559885, 1]
        ]
      },
     "display order":1,
     "estimated parameters":28
    },
   "Nucleotide GTR":{
     "AIC-c":1165.694393932368,
     "Equilibrium frequencies":      [
[0.3348148148148147],
      [0.202962962962963],
      [0.2462962962962963],
      [0.2159259259259259]
      ],
     "Log Likelihood":-559.6409189392783,
     "Rate Distributions":{
       "Substitution rate from nucleotide A to nucleotide C":0.1057602468701381,
       "Substitution rate from nucleotide A to nucleotide G":1,
       "Substitution rate from nucleotide A to nucleotide T":0,
       "Substitution rate from nucleotide C to nucleotide G":0.1465960735122673,
       "Substitution rate from nucleotide C to nucleotide T":2.269319946484975,
       "Substitution rate from nucleotide G to nucleotide T":0.1391184331291334
      },
     "display order":0,
     "estimated parameters":23
    },
   "Unconstrained model":{
     "AIC-c":1164.066233233619,
     "Log Likelihood":-534.6092290289872,
     "Rate Distributions":{
       "Background":{
         "0":{
           "omega":236.9358471479831,
           "proportion":0
          },
         "1":{
           "omega":0.2100294329667581,
           "proportion":0.5542688958966767
          },
         "2":{
           "omega":0.255710153738319,
           "proportion":0.4457311041033233
          },
         "3":{
           "omega":0.2978621753285197,
           "proportion":0
          }
        },
       "Synonymous site-to-site rates":{
         "0":{
           "proportion":0.3409863833415702,
           "rate":0
          },
         "1":{
           "proportion":0.6590136166584298,
           "rate":1.517419329012598
          },
         "2":{
           "proportion":0,
           "rate":1.52677760828329
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        },
       "Test":{
         "0":{
           "omega":226.0589415365084,
           "proportion":0
          },
         "1":{
           "omega":0.04198616898833647,
           "proportion":0.9147510556650086
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         "2":{
           "omega":0.1430120656070995,
           "proportion":0.08477641331245425
          },
         "3":{
           "omega":1,
           "proportion":0.0004725310225371633
          }
        }
      },
     "display order":2,
     "estimated parameters":45
    }
  },
 "input":{
   "file name":"/home/dcallan-adm/Documents/veg/CAPHEINE/work/87/f4fe290e4b23b20d10420f0110f410/capsid_protein_C-nodups.fasta",
   "number of sequences":9,
   "number of sites":100,
   "partition count":1,
   "trees":{
     "0":"(PP563828_1_2023_09_04,PP563831_1_2023_08_29,PP563880_1_2023_10_05,((PP564823_1_2023_10_06,PP563845_1_2023_10_22)Node4,(PP563884_1_2023_09_24,PP563838_1_2023_09_30,PP563839_1_2023_09_29)Node7)Node3,PP563832_1_2023_08_28)"
    }
  },
 "runtime":"2.5.73",
 "substitutions":{
   "0":{
     "0":{
       "root":"ATG"
      },
     "1":{
       "root":"AAC"
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     "10":{
       "root":"CCG"
      },
     "11":{
       "root":"TCT"
      },
     "12":{
       "root":"TTC"
      },
     "13":{
       "root":"AAT"
      },
     "14":{
       "root":"ATG"
      },
     "15":{
       "root":"CTG"
      },
     "16":{
       "root":"AAA"
      },
     "17":{
       "root":"CGC"
      },
     "18":{
       "root":"GCG"
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     "19":{
       "root":"AGA"
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     "2":{
       "root":"AAC"
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     "20":{
       "root":"AAC"
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     "21":{
       "root":"CGC"
      },
     "22":{
       "root":"GTG"
      },
     "23":{
       "root":"TCA"
      },
     "24":{
       "root":"ACT"
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     "25":{
       "PP564823_1_2023_10_06":"GGT",
       "root":"GTT"
      },
     "26":{
       "Node7":"TCA",
       "PP564823_1_2023_10_06":"TCA",
       "root":"CCA"
      },
     "27":{
       "root":"CAG"
      },
     "28":{
       "root":"TTG"
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     "29":{
       "root":"GCG"
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     "3":{
       "root":"CAA"
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     "30":{
       "root":"AAG"
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     "31":{
       "root":"AGA"
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     "32":{
       "root":"TTC"
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     "33":{
       "root":"TCA"
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     "34":{
       "PP563831_1_2023_08_29":"GAA",
       "root":"AAA"
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     "35":{
       "root":"GGA"
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     "36":{
       "root":"TTG"
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     "37":{
       "Node7":"CTT",
       "root":"CTC"
      },
     "38":{
       "PP563884_1_2023_09_24":"TTA",
       "root":"TCA"
      },
     "39":{
       "root":"GGC"
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     "4":{
       "PP563845_1_2023_10_22":"CGA",
       "root":"CGG"
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     "40":{
       "Node4":"CAA",
       "root":"CAG"
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     "41":{
       "root":"GGA"
      },
     "42":{
       "root":"CCC"
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     "43":{
       "root":"ATG"
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     "44":{
       "root":"AAA"
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     "45":{
       "PP563880_1_2023_10_05":"CTA",
       "PP564823_1_2023_10_06":"ATG",
       "root":"CTG"
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     "46":{
       "root":"GTG"
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     "47":{
       "root":"ATG"
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     "48":{
       "root":"GCT"
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     "49":{
       "Node3":"TTC",
       "root":"TTT"
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     "5":{
       "PP564823_1_2023_10_06":"AAG",
       "root":"AAA"
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     "50":{
       "root":"ATA"
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     "51":{
       "root":"GCA"
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     "52":{
       "root":"TTC"
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     "53":{
       "root":"CTA"
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     "54":{
       "root":"AGA"
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     "55":{
       "Node4":"TTT",
       "root":"TTC"
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     "56":{
       "root":"CTA"
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     "57":{
       "root":"GCC"
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     "58":{
       "root":"ATA"
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     "59":{
       "Node3":"CCC",
       "root":"CCT"
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     "6":{
       "root":"AAG"
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     "60":{
       "root":"CCA"
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     "61":{
       "root":"ACA"
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     "62":{
       "root":"GCA"
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     "63":{
       "Node4":"GGA",
       "root":"GGG"
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     "64":{
       "root":"ATT"
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     "65":{
       "root":"TTG"
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     "66":{
       "root":"GCT"
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     "67":{
       "root":"AGA"
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     "68":{
       "root":"TGG"
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     "69":{
       "Node4":"GGC",
       "PP564823_1_2023_10_06":"AGC",
       "root":"GGT"
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     "7":{
       "root":"ACG"
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     "70":{
       "root":"TCA"
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     "71":{
       "root":"TTC"
      },
     "72":{
       "root":"AAG"
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     "73":{
       "root":"AAG"
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     "74":{
       "root":"AAT"
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     "75":{
       "root":"GGA"
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     "76":{
       "root":"GCG"
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     "77":{
       "root":"ATC"
      },
     "78":{
       "root":"AAA"
      },
     "79":{
       "root":"GTG"
      },
     "8":{
       "PP564823_1_2023_10_06":"GGT",
       "root":"GCT"
      },
     "80":{
       "PP563838_1_2023_09_30":"CTG",
       "PP564823_1_2023_10_06":"TTA",
       "root":"CTA"
      },
     "81":{
       "root":"CGG"
      },
     "82":{
       "root":"GGT"
      },
     "83":{
       "PP563832_1_2023_08_28":"TTT",
       "root":"TTC"
      },
     "84":{
       "PP564823_1_2023_10_06":"AAA",
       "root":"AAG"
      },
     "85":{
       "root":"AAA"
      },
     "86":{
       "PP564823_1_2023_10_06":"GAG",
       "root":"GAA"
      },
     "87":{
       "root":"ATC"
      },
     "88":{
       "root":"TCA"
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     "89":{
       "root":"AGC"
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     "9":{
       "root":"CGA"
      },
     "90":{
       "root":"ATG"
      },
     "91":{
       "PP563845_1_2023_10_22":"TTG",
       "root":"CTG"
      },
     "92":{
       "PP564823_1_2023_10_06":"AAC",
       "root":"AAT"
      },
     "93":{
       "root":"ATA"
      },
     "94":{
       "root":"ATG"
      },
     "95":{
       "PP564823_1_2023_10_06":"AAC",
       "root":"AAT"
      },
     "96":{
       "PP564823_1_2023_10_06":"AGG",
       "root":"AGA"
      },
     "97":{
       "root":"AGG"
      },
     "98":{
       "root":"AAA"
      },
     "99":{
       "root":"AGA"
      }
    }
  },
 "test results":{
   "LRT":0,
   "p-value":0.5
  },
 "tested":{
   "0":{
     "Node3":"test",
     "Node4":"test",
     "Node7":"test",
     "PP563828_1_2023_09_04":"background",
     "PP563831_1_2023_08_29":"background",
     "PP563832_1_2023_08_28":"background",
     "PP563838_1_2023_09_30":"background",
     "PP563839_1_2023_09_29":"background",
     "PP563845_1_2023_10_22":"background",
     "PP563880_1_2023_10_05":"background",
     "PP563884_1_2023_09_24":"background",
     "PP564823_1_2023_10_06":"background"
    }
  },
 "timers":{
   "Overall":{
     "order":0,
     "timer":28
    },
   "Preliminary model fitting":{
     "order":1,
     "timer":2
    },
   "Unconstrained BUSTED model fitting":{
     "order":2,
     "timer":25
    }
  }
}